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Structure paper

TitleStructural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 1817, Year 2025
Publish dateFeb 20, 2025
AuthorsYeongmok Lee / Elsa Demes-Causse / Jaemin Yoo / Seo Young Jang / Seoyeon Jung / Justyna Jaślan / Geum-Sook Hwang / Jejoong Yoo / Alexis De Angeli / Sangho Lee /
PubMed AbstractIn plant cells, ALMTs are key plasma and vacuolar membrane-localized anion channels regulating plant responses to the environment. Vacuolar ALMTs control anion accumulation in plant cells and, in ...In plant cells, ALMTs are key plasma and vacuolar membrane-localized anion channels regulating plant responses to the environment. Vacuolar ALMTs control anion accumulation in plant cells and, in guard cells, they regulate stomata aperture. The activation of vacuolar ALMTs depends on voltage and cytosolic malate, but the underlying molecular mechanisms remain elusive. Here we report the cryo-EM structures of ALMT9 from Arabidopsis thaliana (AtALMT9), a malate-activated vacuolar anion channel, in plugged and unplugged lipid-bound states. In all these states, membrane lipids interact with the ion conduction pathway of AtALMT9. We identify two unplugged states presenting two distinct pore width profiles. Combining structural and functional analysis we identified conserved residues involved in ion conduction and in the pore lipid interaction. Molecular dynamics simulations revealed a peculiar anion conduction mechanism in AtALMT9. We propose a voltage-dependent activation mechanism based on the competition between pore lipids and malate at the cytosolic entrance of the channel.
External linksNat Commun / PubMed:39979303 / PubMed Central
MethodsEM (single particle)
Resolution2.63 - 3.7 Å
Structure data

60459

8zte

EMDB-60459, PDB-8zte:
AtALMT9 with LMNG and sterol mimic CHS (sterol1 class)
Method: EM (single particle) / Resolution: 3.17 Å

60461

8ztg

EMDB-60461, PDB-8ztg:
AtALMT9 with LMNG and sterol mimic CHS (sterol2 class)
Method: EM (single particle) / Resolution: 2.95 Å

60462

8zth

EMDB-60462, PDB-8zth:
AtALMT9 with LMNG (narrow class)
Method: EM (single particle) / Resolution: 2.63 Å

60463

8zti

EMDB-60463, PDB-8zti:
AtALMT9 with LMNG (wide class)
Method: EM (single particle) / Resolution: 2.9 Å

60464

8ztj

EMDB-60464, PDB-8ztj:
AtALMT9 with LMNG (cis1-PI4P class)
Method: EM (single particle) / Resolution: 2.73 Å

60465

8ztk

EMDB-60465, PDB-8ztk:
AtALMT9 with LMNG (cis2 class)
Method: EM (single particle) / Resolution: 2.78 Å

60466

8ztl

EMDB-60466, PDB-8ztl:
AtALMT9 with LMNG (intermediate class)
Method: EM (single particle) / Resolution: 2.75 Å

60467

8ztm

EMDB-60467, PDB-8ztm:
AtALMT9 with LMNG (trans1 class)
Method: EM (single particle) / Resolution: 2.84 Å

60468

8ztn

EMDB-60468, PDB-8ztn:
AtALMT9 with LMNG (trans2 class)
Method: EM (single particle) / Resolution: 2.77 Å

61818

9jtw

EMDB-61818, PDB-9jtw:
AtALMT1 with LMNG and sterol mimic CHS
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

ChemComp-MLT:
D-MALATE

ChemComp-HOH:
WATER

ChemComp-D10:
DECANE

ChemComp-PLM:
PALMITIC ACID

ChemComp-OCT:
N-OCTANE

ChemComp-STE:
STEARIC ACID

PDB-1l2f:
Crystal structure of NusA from Thermotoga maritima: a structure-based role of the N-terminal domain

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

Source
  • arabidopsis thaliana (thale cress)
KeywordsMEMBRANE PROTEIN / Plant / Stomata / Vacuole / ALMT / Ion channel / Channel

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